Hiya, I just finished my diy zynthbox with a minimal setup using an esi maya44 Usb Interface (the old USB1 version) . They are pretty cheap on the 2nd hand market and I have a few of them laying around. I was very happy to have 4 individual Inputs as I was mainly interested in the zynthian as an effects box. These jackd Options
-P 70 -t 2000 -s -d alsa -d hw:USB -r 44100 -p 256 -n 3 -S -X raw
made my maya44 work quickly and I was able to see every input in the capture audio menu 
made me very enthusiastic!!!
After patching some effects i finaly realized inputs 3 and 4 are somehow automatically routet to the outputs 1 and 2 (almost as if a harware monitoring switch existet on the interface (which does not). If I enable an effects engine and route the audio of channel 3 or 4 through it, it does work as expected only that the dry bypass to the outputs persists, resulting in the dry signal plus an effected signal. The effected signal does have recognizable latency in comparison to the bypassed signal which makes it pretty unusable this way.
I do remember having similar issues on a clean patchbox install with modep enabled. Here I remeber somehow getting rid of the issues by killing pulseaudio, which I believe is not part of zynthian?!
Any hints are very welcome 
tomorrow i will boot up again and check patchage in a vnc session. hopefully i will gain some insight.
Are you using stable or testing?
Hi riban , I am using stable.
I found the Issue in my mixer settings, which I misunderstood as the 4 individual channels of my interface. Instead Line Left and Line Right appeared to be the dry connection between the inputs 3/4 and outputs 1/2, when I tourned down the levels of these channels I got rid of the permanent connection 
After i found out about this I had still some kind of bleed through of channels 3/4, but after enabling audiolevels on snapshots and disabling Line Levels in the Mixer + turning them down in the webconf and then rebooting — this was gone as well 
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